Facilitated Sequence Counting and Assembly by Template Mutagenesis

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2014 Oct 15

PMID 25313059

Citations 5

Authors

Dan Levy

Michael Wigler

Affiliations

Soon will be listed here.

Abstract

Presently, inferring the long-range structure of the DNA templates is limited by short read lengths. Accurate template counts suffer from distortions occurring during PCR amplification. We explore the utility of introducing random mutations in identical or nearly identical templates to create distinguishable patterns that are inherited during subsequent copying. We simulate the applications of this process under assumptions of error-free sequencing and perfect mapping, using cytosine deamination as a model for mutation. The simulations demonstrate that within readily achievable conditions of nucleotide conversion and sequence coverage, we can accurately count the number of otherwise identical molecules as well as connect variants separated by long spans of identical sequence. We discuss many potential applications, such as transcript profiling, isoform assembly, haplotype phasing, and de novo genome assembly.

Citing Articles

Accurate measurement of microsatellite length by disrupting its tandem repeat structure.

Wang Z, Moffitt A, Andrews P, Wigler M, Levy D Nucleic Acids Res. 2022; 50(20):e116.

PMID: 36095132 PMC: 9723644. DOI: 10.1093/nar/gkac723.

Practical Considerations for Single-Cell Genomics.

Regan C, Preall J Curr Protoc. 2022; 2(8):e498.

PMID: 35926125 PMC: 9479272. DOI: 10.1002/cpz1.498.

Targeted de novo phasing and long-range assembly by template mutagenesis.

Li S, Park S, Ye C, Danyko C, Wroten M, Andrews P Nucleic Acids Res. 2022; 50(18):e103.

PMID: 35822882 PMC: 9561374. DOI: 10.1093/nar/gkac592.

Partial bisulfite conversion for unique template sequencing.

Kumar V, Rosenbaum J, Wang Z, Forcier T, Ronemus M, Wigler M Nucleic Acids Res. 2017; 46(2):e10.

PMID: 29161423 PMC: 5778454. DOI: 10.1093/nar/gkx1054.

Bisulfite-converted duplexes for the strand-specific detection and quantification of rare mutations.

Mattox A, Wang Y, Springer S, Cohen J, Yegnasubramanian S, Nelson W Proc Natl Acad Sci U S A. 2017; 114(18):4733-4738.

PMID: 28416672 PMC: 5422780. DOI: 10.1073/pnas.1701382114.

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